minc-tools 2.1.00-2 / usr / bin / mincpik

#! /usr/bin/env perl
#
# Copyright 2009
# Andrew Janke - a.janke@gmail.com
# The University of Queensland
#
# Permission to use, copy, modify, and distribute this software and its
# documentation for any purpose and without fee is hereby granted,
# provided that the above copyright notice appear in all copies.  The
# author and the University make no representations about the
# suitability of this software for any purpose.  It is provided "as is"
# without express or implied warranty.


use strict;
use warnings "all";
use Getopt::Tabular;
use File::Basename;
use File::Temp qw/ tempdir /;

my($Help, $Usage, $me, @opt_table, $tmpdir, %opt);
my(@args, $args, $infile, $outfile, %ordering, $CODE);

# permutation 'matrix' for differing views
%ordering = (
   'zspace' => ['yspace', 'xspace'],
   'yspace' => ['zspace', 'xspace'],
   'xspace' => ['zspace', 'yspace'],
   );

$me = &basename($0);
%opt = (
   'verbose' => 0,
   'clobber' => 0,
   'fake' => 0,
   
   'slice' => undef,
   'scale' => 2,
   'width' => undef,
   'bitdepth' => 8,
   'range' => undef,
   'image_range' => undef,
   'auto_range' => 0,
   'lookup' => undef,
   'dirs' => ['zspace'],
   
   'triplanar' => 0,
   'tilesize' => 250,
   'title' => 0,
   'title_text' => undef,
   'title_size' => 16,
   'sagittal_offset' => undef,
   'sagittal_offset_perc' => undef,
   'orientation' => 'vertical',
   'anot_bar' => undef,
   );

$Help = <<HELP;
| $me generates image files from MINC volumes using the Imagemagick
|    convert utility. For a complete list of output file types see the
|    convert man pages. (man convert) The resulting image is piped to
|    STDOUT
|
| EXAMPLES:
| To display a default view, transverse slicing, middle slice
| using display. (display is part of the Imagemagick package)
|
|    \$ mincpik infile.mnc PNG:- | display -
|
| To generate a PNG file of the 15th coronal slice
|
|    \$ mincpik -slice 15 -coronal infile.mnc outfile.png
|
| To generate a JPG file using the hotmetal lookup table
|    with the image range 0 to 100
|
|    \$ mincpik -lookup '-hotmetal' -image_range 0 100 infile.mnc outfile.jpg
|
| ImageMagick:  http://www.wizards.dupont.com/cristy/ImageMagick.html
|    NB: ImageMagick should be compiled without 16-bit quanta.
|
| Problems or comments should be sent to: a.janke\@gmail.com
HELP

$Usage = "Usage: $me [options] <infile.mnc> [<image.type>]\n".
         "       $me -help to list options\n\n";

@opt_table = (
   ['-verbose', 'boolean', 0, \$opt{'verbose'},
      'be verbose'],
   ['-clobber', 'boolean', 0, \$opt{'clobber'},
      'overwrite existing files'],
   ['-fake', 'boolean', 0, \$opt{'fake'},
      'do a dry run, (echo cmds only)' ],
   ['-slice', 'integer', 1, \$opt{'slice'},
      'slice number to get',
      '<int>'],
   ['-scale', 'integer', 1, \$opt{'scale'},
      'scaling factor for resulting image',
      '<int>'],
   ['-width', 'integer', 1, \$opt{'width'},
      'autoscale the image to have a fixed image width (in pixels)',
      '<int>'],
   ['-depth', 'integer', 1, \$opt{'bitdepth'},
      'bitdepth for resulting image 8 or 16 (MSB machines only!)',
      '<int>'],
   ['-title', "boolean", 0, \$opt{'title'},
      "add a title to the resulting image"],
   ['-title_text', "string", 1, \$opt{'title_text'},
      "use <string> for the title [default: input-filename]",
      "<string>"],
   ['-title_size', "integer", 1, \$opt{'title_size'},
      "font point size for the title",
      "<int>"],
   ['-anot_bar', "string", 1, \$opt{'anot_bar'},
      "create an annotated bar to match the image (use height of the output image)",
      "<fname.png>"],
   
   ['Image range and lookup table options', 'section' ],
   ['-range', 'float',   2, \@{$opt{'range'}},
      'valid range of values for MINC file',
      '<real> <real>'],
   ['-image_range', 'float', 2, \@{$opt{'image_range'}},
      'range of image values to use for pixel intensity',
      '<real> <real>'],
   ['-auto_range', 'boolean', 0, \$opt{'auto_range'},
      'automatically determine image range'],
   ['-lookup', 'string', 1, \$opt{'lookup'},
      'arguments to pass to minclookup',
      '<\'argument list\'>'],
   
   ['Slicing options', 'section' ],
   ['-transverse', 'arrayconst', ['zspace'], \@{$opt{'dirs'}},
      'get a transverse slice'],
   ['-axial', 'arrayconst', ['zspace'], \@{$opt{'dirs'}},
      'synonym for transverse'],
   ['-coronal', 'arrayconst', ['yspace'], \@{$opt{'dirs'}},
      'get a coronal slice'],
   ['-sagittal', 'arrayconst', ['xspace'], \@{$opt{'dirs'}},
      'get a sagital slice'],
   ['-allthree', 'arrayconst', ['zspace', 'xspace', 'yspace'], \@{$opt{'dirs'}},
      'you probably dont want this, it is somewhat broken, use -triplanar instead'],
   
   ['triplanar options', 'section' ],
   ['-triplanar', 'boolean', 0, \$opt{'triplanar'},
      'create a triplanar view of the input MINC file'],
   ['-tilesize', "integer", 1, \$opt{'tilesize'},
      "pixel size for each image in a triplanar"],
   ['-sagittal_offset', "integer", 1, \$opt{'sagittal_offset'},
      "offset the sagittal slice from the centre",
      "<# slices>"],
   ['-sagittal_offset_perc', "integer", 1, \$opt{'sagittal_offset_perc'},
      "offset the sagittal slice by a percentage from the centre",
      "<% offset>"],
   ['-vertical', 'const', 'vertical', \$opt{'orientation'},
     'create a vertical triplanar view (Default)'],
   ['-horizontal', 'const', 'horizontal', \$opt{'orientation'},
     'create a horizontal triplanar view'],
   );

# Check arguments
&Getopt::Tabular::SetHelp ($Help, $Usage);
&GetOptions (\@opt_table, \@ARGV) || exit 1;
die $Usage if ($#ARGV < 0);

# create temporary directory
$tmpdir = &tempdir( "$me-XXXXXXXX", TMPDIR => 1, CLEANUP => 1 );

# set up file names and do a few checks
$infile = $ARGV[0];
$outfile = (defined($ARGV[1])) ? $ARGV[1] : 'PNG:-';

die "$me: Couldn't find $infile\n\n" if (!-e $infile);
if($outfile ne 'PNG:-' && -e $outfile && !$opt{'clobber'}){
   die "\n$me: $outfile exists, use -clobber to overwrite\n\n";
   }

if($opt{'bitdepth'} != 16 && $opt{bitdepth} != 8) {
   die "\n$me: Invalid bitdepth specified - $opt{bitdepth} instead of 8 or 16\n\n";
   }

# sanity check
if($opt{'auto_range'} && @{$opt{'image_range'}}){
   die "\n$me: only specify one of -auto_range and -image_range (not both)\n\n";
   }

# warn about -slice and -triplanar
if(defined($opt{'slice'}) && $opt{'triplanar'}){
   warn "\n$me: you probably don't want to use both -triplanar and -slice\n\n";
   } 

# warn about -sagittal_offset and -sagittal_offset_perc
if(defined($opt{'sagittal_offset'}) && $opt{'sagittal_offset_perc'}){
   warn "\n$me: only use one of -sagittal_offset -sagittal_offset_perc\n\n";
   } 

# set up directions for triplanar
if($opt{'triplanar'}){
   $opt{'dirs'} = ['zspace', 'xspace', 'yspace'];
   }

my ($space, $n_slices, $convert_infile, $imgfile,
    @extract_args, @convert_args,
    $img_x, $img_y,
    $img_step_x, $img_step_y, 
    $img_length_x, $img_length_y,
    $dim_names, $pipe_args, $dimorder,
    @mont_files);

# find the 5% to 95% PcT image range if -auto_range
if($opt{'auto_range'}){
   my $buf;
   
   print STDERR "Getting range of $infile\n" if $opt{'verbose'};
   
   chomp($buf = `mincstats -quiet -pctT 5 $infile`);
   $buf *= 1.0;
   @{$opt{'image_range'}}[0] = $buf;

   chomp($buf = `mincstats -quiet -pctT 95 $infile`);
   $buf *= 1.0;
   @{$opt{'image_range'}}[1] = $buf;

   # a bit of output
   if($opt{'verbose'}){
      print STDERR "Using image range of [@{$opt{image_range}}[0]:@{$opt{image_range}}[1]]\n";
      }
   }

# foreach slicing direction
foreach $space (@{$opt{'dirs'}}){

   print STDERR "Doing direction $space\n" if $opt{'verbose'};
   
   my($slice);
   $CODE = "GRAY";
   
   # set up the imgfile depending on triplanar and -title
   if($opt{'triplanar'}){
      $imgfile = "$tmpdir/trip-$space.png";
      push(@mont_files, $imgfile);
      }
   elsif($opt{'title'}){
      $imgfile = "$tmpdir/image.png";
      }
   else{
      $imgfile = $outfile;
      }
   
   # Get the info we need
   $args = "mincinfo ".
           "-dimlength $space ".
           "-dimlength $ordering{$space}[0] ".
           "-dimlength $ordering{$space}[1] ".
           "-attvalue $ordering{$space}[0]:step ". 
           "-attvalue $ordering{$space}[1]:step ".
           "-dimnames ".
           $infile;
   ($n_slices, $img_x, $img_y, $img_step_x, $img_step_y, $dim_names) = split("\n", `$args`);

   if(defined($opt{'width'})){ 
      $opt{'scale'} = $opt{'width'}/abs($img_step_y * $img_y);
      print STDERR "Auto-scaling width factor: $opt{'scale'}\n" if $opt{'verbose'}; 
      }
   $img_length_x = abs(int($img_step_x * $img_x * $opt{'scale'}));
   $img_length_y = abs(int($img_step_y * $img_y * $opt{'scale'}));
   
   # figure out the slice to get
   $slice = (!defined($opt{'slice'})) ? int($n_slices/2) : $opt{'slice'};
   
   # do the sagittal offset (only one of these should be done)
   if($space eq 'xspace'){

      # slice offset      
      if(defined($opt{'sagittal_offset'})){
         $slice += $opt{'sagittal_offset'};
         }

      # perc offset
      if(defined($opt{'sagittal_offset_perc'})){
         $slice += int($n_slices * $opt{'sagittal_offset_perc'} / 100);
         }
      }
   
   # check we didn't step of the edge
   if($slice >= $n_slices || $slice < 0){ 
      die "Slice $slice out of range (0-" . ($n_slices-1) . ")\n\n";
      }
   
   # check if we have a vector_dimension already
   if($dim_names =~ m/vector_dimension/){
      $CODE = 'RGB';
      }
  
   # take only the first timepoint if we have a time dimension
   my @time_res_args = ();
   if($dim_names =~ m/time/){
      @time_res_args = ('-dimrange', "time=0,0");
      }
    
   # do the reshaping
   $dimorder = join(',', $space, @{$ordering{$space}});
   if($CODE eq 'RGB'){
      $dimorder .= ',vector_dimension';
      }
   @args = ('mincreshape', '-clobber', '-quiet',
            '-normalize',
            '+direction',
            '-dimsize', "$space=-1",
            '-dimsize', "$ordering{$space}[0]=-1",
            '-dimsize', "$ordering{$space}[1]=-1",
            '-dimorder', $dimorder,
            '-dimrange', "$space=$slice,1",
            @time_res_args,
            $infile, "$tmpdir/reshaped.mnc");                  
   if(scalar(@{$opt{'range'}}) != 0){
      push(@args, '-valid_range', @{$opt{'range'}}[0], @{$opt{'range'}}[1]);
      }
   if(scalar(@{$opt{'image_range'}}) != 0){
      push(@args, '-image_range', @{$opt{'image_range'}}[0], @{$opt{'image_range'}}[1]);
      }
   &do_cmd(@args);
   
   # do the lookup if required
   $convert_infile = "$tmpdir/reshaped.mnc";
   if($opt{'lookup'}){
      if($CODE eq 'RGB'){
         warn "$me: Input is vector-valued already.  No colour lookup done.\n";
         }
      else{
         $convert_infile = "$tmpdir/lookup.mnc";
         $CODE = 'RGB';
         &do_cmd('minclookup', '-clobber', '-quiet', 
                 split(' ', $opt{'lookup'}), 
                 "$tmpdir/reshaped.mnc", $convert_infile);
         }
      }

   # set up mincextract command
   @extract_args = ('mincextract', $convert_infile,
                    '-normalize',
                    ($opt{'bitdepth'} == 16) ? ('-short', '-unsigned') : '-byte');
   
   # set up convert arguments
   # a flip is 'normal' due to the difference between mnc and most image co-ordinates
   @convert_args = ('convert',
                    '-depth', $opt{'bitdepth'},
                    '-flip', 
                    '-size', $img_y . 'x' . $img_x,
                    '-geometry', $img_length_y . 'x' . $img_length_x . '!',
                    "$CODE:-", $imgfile);
   
   # check if we are big or little endian for convert's MSB wierdity
   $pipe_args = '|';
   if($opt{'bitdepth'} == 16){
      if(unpack("c",substr(pack("s",1),0,1))){
         warn "$me: LSB machine, swapping bytes with dd and crossing fingers\n";
         $pipe_args .= ' dd conv=swab | ';
         }
      }
   
   &do_cmd(join(' ', @extract_args, $pipe_args, @convert_args));
   }

# do the triplanar if requested
if($opt{'triplanar'}){
   my @orient_args;

   if($opt{'title'}){
      $imgfile = "$tmpdir/mont.png";
      }
   else{
      $imgfile = $outfile;
      }
   
   if($opt{'orientation'} eq 'vertical'){
      @orient_args = ('-tile', ('1x' . ($#mont_files + 1)));
      }
   else{ # $opt{orientation} eq 'horizontal'
      @orient_args = ('-tile', (($#mont_files + 1) . 'x1'));
      }
   
   # do the montage
   &do_cmd('montage',
           @orient_args, 
           '-background', 'grey10',
           '-geometry', "$opt{tilesize}x$opt{tilesize}+1+1",
           @mont_files, $imgfile);
   }
               
# Add the title
if($opt{'title'}){
   
   # set up the title text
   if(!defined($opt{'title_text'})){
      $opt{'title_text'} = &basename($infile);
      $opt{'title_text'} =~ s/\.mnc$//;
      }
     
#   This really does not work all that well (but should), go figure
#   &do_cmd('convert', '-box', 'black', 
#           '-font', '7x13', 
#           '-fill', 'white',
#           '-draw', "text 4,12 \"$opt{'title_text'}\"",
#           $imgfile, $outfile);
#
   # use montage instead
   &do_cmd('montage', 
           '-geometry', '100x100%',  
           '-background', 'black',
           '-fill', 'white',
           '-label', $opt{'title_text'},
           '-pointsize', $opt{'title_size'},
           $imgfile, $outfile);
   }

# create the annotated bar if required
if(defined($opt{'anot_bar'})){
   
   my($min, $max, $pcode, 
      $q0, $q1, $q2, $q3, $q4, $bh, $bw, $bb, $ob, 
      $textbump, $i, @buf);
   
   # set up a few constants
   $textbump = 3;
   $pcode = '%6g';
   
   # text border, other border, height, width
   $bb = 50;
   $ob = 25;
   $bh = $img_length_y - ($ob*2);
   $bw = int($bh/10);
   
   # get range if not defined
   if(!defined(@{$opt{'image_range'}[0]})){
      print STDERR "Getting image range\n" if $opt{'verbose'};
      
      @buf = split(/\n/, `mincstats -min -max -quiet $infile`);
      @{$opt{'image_range'}}[0] = $buf[0] * 1.0;
      @{$opt{'image_range'}}[1] = $buf[1] * 1.0;
      }
   
   $min = @{$opt{'image_range'}}[0];
   $max = @{$opt{'image_range'}}[1];
   
   # set up the datafile
   my(@data) = undef;
   my($packstring) = '';
   for($i=0; $i<$bh; $i++){
      $data[$i] = $i;
      $packstring .= 'f';
      }
   
   open(FH, ">$tmpdir/tmp-float.raw");
   for($i=0; $i<$bw; $i++){
      syswrite(FH, pack($packstring, @data));
      }
   close(FH);
   
   # make minc file
   &do_cmd('rawtominc', '-clobber',
           '-float',
           '-input', "$tmpdir/tmp-float.raw",
           '-xstep',  1, '-ystep',  1, '-zstep',  1,
           '-xstart', 0, '-ystart', 0, '-zstart', 0,
           '-dimorder', 'xspace,yspace,zspace',
           "$tmpdir/bar.mnc", $bw, $bh, 1);
   

   # make .miff bar image (whoa... recursion!)
   &do_cmd('mincpik', '-clobber',
           '-scale', 1,
           (defined($opt{'lookup'})) ? ('-lookup', $opt{'lookup'}) : (),
           "$tmpdir/bar.mnc", "$tmpdir/bar.png");
   
   # set up the text
   $q0 = sprintf($pcode, $min);
   $q1 = sprintf($pcode, (($max-$min) * 0.25) + $min);
   $q2 = sprintf($pcode, (($max-$min) * 0.5)  + $min);
   $q3 = sprintf($pcode, (($max-$min) * 0.75) + $min);
   $q4 = sprintf($pcode, $max);
   
   
   # create the bar itself via convert
   &do_cmd('convert',
           '-bordercolor', 'white',
           '-border', $bb,

           # color for all the decorations
           '-fill', 'black',

           # bar border
           '-draw', "line " . join(',',  $bb,      $bb,      ($bb+$bw),  $bb     ),
           '-draw', "line " . join(',',  $bb,     ($bb+$bh), ($bb+$bw), ($bb+$bh)),
           '-draw', "line " . join(',',  $bb,      $bb,       $bb,      ($bb+$bh)),
           '-draw', "line " . join(',', ($bb+$bw), $bb,      ($bb+$bw), ($bb+$bh)),

           # 3 ticks at 1/4, 1/2 and 3/4
           '-draw', "line " . join(',', ($bb+($bw*3/4)), ($bb+($bh*1/4)), ($bb+$bw), ($bb+($bh*1/4))),
           '-draw', "line " . join(',', ($bb+($bw*3/4)), ($bb+($bh*2/4)), ($bb+$bw), ($bb+($bh*2/4))),
           '-draw', "line " . join(',', ($bb+($bw*3/4)), ($bb+($bh*3/4)), ($bb+$bw), ($bb+($bh*3/4))),

           # text
           '-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*0/4)+$textbump) . " '$q4'",
           '-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*1/4)+$textbump) . " '$q3'",
           '-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*2/4)+$textbump) . " '$q2'",
           '-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*3/4)+$textbump) . " '$q1'",
           '-draw', 'text ' . ($bb+$bw) . ',' . ($bb+($bh*4/4)+$textbump) . " '$q0'",

           # finally crop of the extra border
           '-crop', (($bb*2)+$bw-($bb-$ob)) . "x" . (($bb*2)+$bh-$bb) . "+" . ($bb-$ob) . "+" . ($bb-$ob),

           "$tmpdir/bar.png", $opt{'anot_bar'});
   }


sub do_cmd {
   print STDERR "@_\n" if $opt{'verbose'};
   if(!$opt{'fake'}){
      system(@_) == 0 or die "\n$me: Failed executing @_\n\n";
      }
   }